[permissions] fix workflows + remove shouldBypassPermissionChecks for system objects (#12559)

In this PR 

1. fix workflow step creation by adding forgotten
`shouldBypassPermissionChecks` in WorkflowVersionStepWorkspaceService
2. clarify the rule for twentyORMGlobalManager: do not add unnecessary
`shouldBypassPermissionChecks` for system objects (there are no
object-records permission checks on system objects, they are dealt with
at resolver level)

packages/twenty-server/src/database/commands/upgrade-version-command/0-54/0-54-clean-not-found-files.command.ts

@@ -188,6 +188,7 @@ export class CleanNotFoundFilesCommand extends ActiveOrSuspendedWorkspacesMigrat
       await this.twentyORMGlobalManager.getRepositoryForWorkspace<PersonWorkspaceEntity>(
         workspaceId,
         'person',
+        { shouldBypassPermissionChecks: true },
       );
     const people = await personRepository.find({
       where: {

packages/twenty-server/src/database/commands/upgrade-version-command/0-55/0-55-deduplicate-indexed-fields.command.ts

@@ -73,6 +73,7 @@ export class DeduplicateIndexedFieldsCommand extends ActiveOrSuspendedWorkspaces
       await this.twentyORMGlobalManager.getRepositoryForWorkspace(
         workspaceId,
         'company',
+        { shouldBypassPermissionChecks: true },
       );
 
     const duplicates = await companyRepository
@@ -121,6 +122,7 @@ export class DeduplicateIndexedFieldsCommand extends ActiveOrSuspendedWorkspaces
       await this.twentyORMGlobalManager.getRepositoryForWorkspace(
         workspaceId,
         'person',
+        { shouldBypassPermissionChecks: true },
       );
 
     const duplicates = await personRepository